Ok everyone, I'm new to this so please be nice. I am trying to update Bioconductor in my R. I have R 3.3.0. I followed the troubleshooting instructions to load with R --vanilla and remove.packages (biocInstaller) etc. and it still doesn't work. And I have looked at other posts where other people have struggled and I still can't seem to figure it out.

Bioconductor version 3.0 (BiocInstaller 1.16.5), ?biocLite. for help
BiocInstaller version 3.0 is too old for R version 3.3.0;
remove.packages("BiocInstaller") then
source("http://bioconductor.org/biocLite.R")
A new version of Bioconductor is available after
installing the most recent version of R; seehttp://bioconductor.org/install

I have tried this in several R sessions. Also, I run biocValid() and the same packages (179 of them) are out of date every time, so it's not saving the updated ones after running biocLite() ?

It seems likely that your R was installed as 'Administrator', that there are at least two library paths

.libPaths()

and that one of them is not writable by the user you are currently running as. The R error message "there is no package called 'BiocInstaller'" is I think R's way of saying "...that I can remove".

I would suggest simply starting with a new R installation, installed as a regular user.

The alternative is to run R as an 'Administrator' and update your Administrator packages, then switch back to your usual user and update the out-of-date packages. But this only perpetuates the problem, and you'll have to run as Administrator periodically.

Thank you for sharing that! There are 2 paths -one under the Program Files (administrator) which has a library and the exe files, and one where I have my package library under my user. I think I have to re-install R because trying to move things I caused the 'fatal error: no base package' message. Is it regular practice to have two copies of the library like that? Maybe I've just been updating my R wrong every time...

There is always a library path associated with the location R is installed, e.g., under Program Files. If R detects that the current user can't install packages at that location, it will ask whether it is OK to create a second path, and will remember that the second path exists. So two paths are normal when R has been installed as one user, and used as another.

For individual workstations, it is better to install R under your regular user account. There will then be a single library path, and all packages can be updated by the regular user.